JAL-3725 restrict mapped virtual feature location to mapped region

[jalview.git] / src / jalview / io / BioJsHTMLOutput.java

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index fd9c584..9db3df2 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -20,7 +20,6 @@
  */
 package jalview.io;
 
-import jalview.exceptions.NoFileSelectedException;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.OOMWarning;
 import jalview.json.binding.biojs.BioJSReleasePojo;
@@ -41,7 +40,6 @@ import java.util.TreeMap;
 
 public class BioJsHTMLOutput extends HTMLOutput
 {
-
   private static File currentBJSTemplateFile;
 
   private static TreeMap<String, File> bioJsMSAVersions;
@@ -53,44 +51,14 @@ public class BioJsHTMLOutput extends HTMLOutput
           .getDefault("biojs_template_directory", DEFAULT_DIR);
 
   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
-          .getDefault(
-                  "biojs_template_git_repo",
+          .getDefault("biojs_template_git_repo",
                   "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
 
   public BioJsHTMLOutput(AlignmentPanel ap)
   {
-    super(ap);
+    super(ap, "BioJS MSA");
   }
 
-  @Override
-  public void exportHTML(String outputFile)
-  {
-    exportStarted();
-    try
-    {
-      if (outputFile == null)
-      {
-        outputFile = getOutputFile();
-      }
-      generatedFile = new File(outputFile);
-    } catch (NoFileSelectedException e)
-    {
-      setProgressMessage(MessageManager.formatMessage(
-              "status.cancelled_image_export_operation", "BioJS MSA"));
-      return;
-    } catch (Exception e)
-    {
-      setProgressMessage(MessageManager.formatMessage(
-              "info.error_creating_file", "BioJS MSA"));
-      e.printStackTrace();
-      return;
-    }
-    new Thread(this).start();
-
-  }
-
-
-
   public static void refreshVersionInfo(String dirName)
           throws URISyntaxException
   {
@@ -133,7 +101,8 @@ public class BioJsHTMLOutput extends HTMLOutput
       {
         try
         {
-          String gitRepoPkgJson = getURLContentAsString(BJS_TEMPLATE_GIT_REPO);
+          String gitRepoPkgJson = getURLContentAsString(
+                  BJS_TEMPLATE_GIT_REPO);
           if (gitRepoPkgJson != null)
           {
             BioJSRepositoryPojo release = new BioJSRepositoryPojo(
@@ -235,8 +204,8 @@ public class BioJsHTMLOutput extends HTMLOutput
         }
       }
     }
-    return responseStrBuilder == null ? null : responseStrBuilder
-            .toString();
+    return responseStrBuilder == null ? null
+            : responseStrBuilder.toString();
   }
 
   public static File getCurrentBJSTemplateFile()
@@ -273,12 +242,6 @@ public class BioJsHTMLOutput extends HTMLOutput
   }
 
   @Override
-  public File getExportedFile()
-  {
-    return generatedFile;
-  }
-
-  @Override
   public void run()
   {
     try
@@ -289,13 +252,13 @@ public class BioJsHTMLOutput extends HTMLOutput
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
               .replaceAll("#sequenceData#", bioJSON).toString();
 
-      PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
-              generatedFile));
+      PrintWriter out = new java.io.PrintWriter(
+              new java.io.FileWriter(generatedFile));
       out.print(generatedBioJsWithJalviewAlignmentAsJson);
       out.flush();
       out.close();
-      setProgressMessage(MessageManager.formatMessage(
-              "status.export_complete", "BioJS"));
+      setProgressMessage(MessageManager
+              .formatMessage("status.export_complete", getDescription()));
       exportCompleted();
 
     } catch (OutOfMemoryError err)
@@ -305,8 +268,8 @@ public class BioJsHTMLOutput extends HTMLOutput
       new OOMWarning("Creating Image for " + generatedFile, err);
     } catch (Exception e)
     {
-      setProgressMessage(MessageManager.formatMessage(
-              "info.error_creating_file", "HTML"));
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
       e.printStackTrace();
     }